There are many differences in syntax between Blackfriday’s Markdown and Pandoc’s Markdown. For example, you can write a task list with Blackfriday but not with Pandoc:

Write an R package.

Write a book.

…

Profit!

Similarly, Blackfriday does not support LaTeX math and Pandoc does. I have added the MathJax support to this theme (hugo-xmin) but there is a caveat for plain Markdown posts: you have to include math expressions in a pair of backticks (inline: `$ $`; display style: `$$ $$`), e.g., $S_n = \sum_{i=1}^n X_i$.1 For R Markdown posts, you do not need the backticks, because Pandoc can identify and process math expressions.

When creating a new post, I recommend you to use the RStudio addin “New Post”: